A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
This report has been generated by the nf-core/aquascope analysis pipeline. For information about how to interpret these results, please see the documentation.
Report
generated on 2024-11-02, 18:18 EDT
based on data in:
/scicomp/scratch/xuz1/nextflow/work/49/ff96f8827e7eccf0d8e9a233486c3e
General Statistics
| Sample Name | Top lineage | Top lineage % |
|---|---|---|
| Sample1 | XBB.1.5* [Omicron (XBB.1.5.X)] | 76.8% |
| Sample2 | XBB* (XBB.X) | 71.6% |
NWSS/aquascope Methods Description
Suggested text and references to use when describing pipeline usage within the methods section of a publication.
Methods
Data was processed using NWSS/aquascope v3.0 (doi: ) of the nf-core collection of workflows (Ewels et al., 2020).
The pipeline was executed with Nextflow v24.04.2 (Di Tommaso et al., 2017) with the following command:
nextflow run main.nf --resume -profile singularity,test_bam -entry FREYJA_ONLY --outdir ~/projects/tmp/aqua//freyjaReferences
- Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. https://doi.org/10.1038/nbt.3820
- Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. https://doi.org/10.1038/s41587-020-0439-x
Notes:
- The command above does not include parameters contained in any configs or profiles that may have been used. Ensure the config file is also uploaded with your publication!
- You should also cite all software used within this run. Check the "Software Versions" of this report to get version information.
CDCGov-Aquascope Workflow Summary
- this information is collected when the pipeline is started.
Core Nextflow options
- runName
- stupefied_keller
- containerEngine
- singularity
- launchDir
- /scicomp/home-pure/xuz1/projects/aqua/aquascope
- workDir
- /scicomp/scratch/xuz1/nextflow/work
- projectDir
- /scicomp/home-pure/xuz1/projects/aqua/aquascope
- userName
- xuz1
- profile
- singularity,test_bam
- configFiles
- N/A
Input/output options
- input
- /scicomp/home-pure/xuz1/projects/aqua/aquascope/assets/samplesheet_test_bam.csv
- outdir
- ~/projects/tmp/aqua//freyja
Institutional config options
- config_profile_name
- Test BAM input
- config_profile_description
- Minimal test dataset to check pipeline function
Max job request options
- max_cpus
- 2
- max_memory
- 6 GB
- max_time
- 6h
Other parameters
- gff3
- /scicomp/home-pure/xuz1/projects/aqua/aquascope/assests/references/SARS-CoV-2.reference.gff3
- hostnames
- {}
Freyja
Freyja Recover relative lineage abundances from mixed SARS-CoV-2 samples.DOI: 10.1038/s41586-022-05049-6.
Freyja Summary
Relative lineage abundances from mixed SARS-CoV-2 samples. Hover over the column headers for descriptions and click Help for more in-depth documentation.
The graph denotes a sum of all lineage abundances in a particular WHO designation , otherwise they are grouped into "Other". Lineages abundances are calculated as the number of reads that are assigned to a particular lineage. Lineages and their corresponding abundances are summarized by constellation.
Note: Lineage designation is based on the used WHO nomenclature, which could vary over time.
